If we go back a bit, the original TP scheme was (apparently) costed just for the wiring of the as-is line, nothing else, no upgrades, resignalling etc.
So DfT (pre-Grayling) "paused" the scheme when it realised there would be no journey time improvements, and asked for a range of upgrade options.
By the time NR had done this, the electrification budget had been broken by GW anyway, so it stayed paused and even Vic-Stalybridge was severely cut back.
Now we are talking about a £2.9 billion budget for a full scheme (route upgrade with partial wiring).
It's clear this that figure is from the Northern Powerhouse pipeline and won't change, so the task is to get the best result for that money.
Once again it's not how to start a major project, any more than it was for the GW scheme (or HS2!).
But it's where we are. If NR can reduce full wiring costs (or other project scope) so that it can be delivered within the budget, then it will be done.
Otherwise, bi-modes win the day.
If you read Roger's piece, it's not about suppliers cutting margins, it's about design standards (clearances, piling strategy etc).